Phages are the most abundant biological entities on the planet and have had tremendous impact on biological sciences; however, phage genomes lag behind bacterial and eukaryotic genomes in the quality of annotation. For this purpose, the PhAnToMe project was launched to establish a phage annotation database, a rapid annotation pipeline for phage genomes (PhiRAST or phage Rapid Annotation Using Subsystem Technology), and a graphic programming interface for biologists (using the BioBIKE interface).
The PhAnToMe project involves multiple research centers in the United States and includes several stages. The SDSU center is in charge of developing phage genomic subsystems, phage protein families (FIGFams), and subsequently the first release of PhiRAST. As a member of this team, I am in charge of building or coordinating subsystems, and of establishing links with the phage research community. In addition, once the PhiRAST is developed, I will also be in charge of coordinating training workshops and developing testable hypotheses based on the PhAnToMe annotations and subsystems.
The lab’s spearhead PhAnToMe project is funded by the National Science Foundation to understand viral life. We are researching the genomics of viruses that infect bacteria — phages — with Dr. Mya Breitbart (Univ. Southern Florida), Dr. Matt Sullivan (U. Arizona), and Dr. Jeff Elhai (Virginia Commonwealth University). These viruses are the most abundant biological entities on the planet, and are responsible for many of the evolutionary changes that bacteria undergo. Phages carry virulence genes that allow bacteria to cause disease, they carry photosynthetic genes that allow bacteria to grow in the oceans, and they carry many genes that we don’t even know what they do. Our project will unearth the role of some of those genes and proteins, and help biologists get to grips with the most diverse parts of microbiology — the phages. At the PhAnToMe website you can browse complete genomes, and download phage genomes and associated data.
Rob Edwards’ bioinformatics lab at San Diego State University is all about decoding life’s best kept secrets. These secrets are encoded, as you must have already guessed, in genomes of bacteria, archaea, eukaryotes and the viruses that infect them.
We use all kinds of computers, from clusters to cell phones, to solve the most unsolvable computational problems that help us better understand biology.
Rob has collaborations all over the world, and has taught in Europe, Asia, and Latin America. We are currently funded by the Department of Education through the Fund for the Improvement of Postsecondary Education and the Brazilian Ministry of Education (FIPSE-CAPES) to develop a marine sciences course in Brazil.
Rob has published over 60 peer-reviewed papers, and given an equal number of talks. A short biography about Rob describes his background, and his CV has more information. You can contact Rob for more information.